


The Heart of Sherlock Holmes

by Noddifer



Series: The Heart of Sherlock Holmes [1]
Category: Sherlock (TV)
Genre: Alternate Universe, BAMF Mary, BAMF Molly, Emotional Hurt/Comfort, Gen, Hurt/Comfort, Kidnapping, Non-Graphic Rape/Non-Con, Torture
Language: English
Status: In-Progress
Published: 2014-04-06
Updated: 2014-11-18
Packaged: 2018-01-18 10:09:21
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 6
Words: 8,152
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1424608
Author URL: https://archiveofourown.org/users/Noddifer/pseuds/Noddifer
Summary: <blockquote class="userstuff">
              <p>John has always known that Sherlock Holmes could love.</p>
            </blockquote>





	1. Part 1

_As always I have no rights but I play with them anyway._

** **Part 1** **

 

John has always known that Sherlock Holmes could love. It’s not a very big secret, even though his old room mate seems to act like it is. Actions are louder than words after all and Sherlock is a man of action.

John could probably start a new blog dedicated to the ways that Sherlock shows affection, but he won’t. That knowledge has to be  _earned._

His sociopathic ex-room mate does not come with an instruction manual. Though the doctor doubts that would ever be useful given Sherlock’s ever changing behaviour.  _Bi-polar_ was his first impression… followed by Autistic. Much later, John gave up trying to pin a label. Nothing was ever going to fit properly.

 

So when Sherlock forcefully reminds his friend time and time again that he doesn’t have friends, that he doesn’t have it in him to be sentimental or loving. The doctor has to bite his tongue and refrain from rolling his eyes in a truly sherlockian fashion. Unfortunately (or fortunately, he can never decide) his wife doesn’t share the same self-control and outwardly laughs at the detectives childish outbursts before patting him on the head in a motherly fashion.

John does have to make himself busy with tea when Sherlock huffs and storms into his room in a sulk.

Sherlock Holmes: The Giant Toddler.

There’s another reason he’s never written the brutal honesty about his friend, Sherlock would undoubtedly find out and proclaim war on him. It’s not worth it seeing what he’s like with Mycroft. The battles would be bloody and he values his peace far too much for that.

  
  
The one thing John has never been sure about though, in the many years he has known Sherlock, is the detectives feelings for Molly.

 

She’s stronger than he gave her credit for. On his introduction to her, he’s ashamed to admit that he initially though her to be meek and easily controlled. He had felt appalled at how easy it must be for both Moriarty and Sherlock to control her the way they do. The following Christmas, he had felt sorry for the cruel way in which his friend laid latched into her nerve and left it for all to see. In that moment John had realised how deep Sherlock’s brutality could go.

Molly had surprised him then, in a small voice she had made Sherlock see the error in his ways. How his intelligence could destroy those that cared for him. She had awoken him to what so many others had failed to do. In that moment John had been in awe of her strength.

After the fall, John doesn't think of her as he did at the beginning. He would never imagine her to be that way any more. She’s too important and too commanding of Sherlock, to let that initial impression stick. She makes him apologise, slaps him when he’s gone beyond what even she deems expectable of him. She silences him with _a look,_ a fleeting _glance_ and he’s quiet mid-insult.

John has never seen Sherlock do that with anyone. Not even his mother.

  
  
Lestrade is another matter. He’s like a really awesome uncle, the one that you wish you could live with when you are a child.

He indulges Sherlock’s thirst for knowledge. Allows him unprecedented access to crime scenes and listens to the Consultant Detective’s rather unusual methods. He’s a good friend who bails them out of jail for his stag do, but isn’t above making them pay slightly for not including him. Greg is unusually acceptive of all of them for who they are, quirks and all, and doesn’t judge. He even protects them other’s who are not so understanding.

He can clearly see why Sherlock loves the man. Even if neither of them will ever admit it under duress.

  
  
After the Appledore incident, Sherlock is a changed man. John had worried that he would revert to his cold, hard-hearted days as coping mechanism for having his heart exposed to the world.

He had never been so wrong.

Sherlock is fiercely protective of everyone in his inner circle. He has Mycroft use his resources to watch them, has them followed everywhere and uses his own homeless network as a protection detail. John receives countless texts verifying his location and Mary has to talk him out of tagging the baby. John’s urge to shoot him becomes increasingly justified until Molly goes missing.

At first everyone thinks it’s an error. That someone has messed up somewhere in the network. Sherlock, in true character, rips through all the data to find the mistake. There isn't one. He then attacks Mycroft’s people and sifts through them with devastating results. Mycroft has a mole, but they are not involved with Molly. Sherlock forces Lestrade to investigate his force and is enraged when nothing becomes of it than the usual. To placate him, Greg goes against protocol and gives him full access to all the evidence in Scotland Yard. They find nothing of use and Mary voices her concerns for their friends increasingly worrying behaviour.

John seriously considers letting Sherlock tag his child.

  
  
Its after Scotland Yard transfers Molly’s case to another department and the months rack up that John wakes up the truth of who Molly is Sherlock. He feels rather silly that it has taken him so long to work it out and Mary squeezes his shoulders in a pacifying gesture.

Later as he forces Sherlock to eat something and to sleep for an hour in his chair, he promises his friend that they will find Molly. They won’t give up, no matter what. That night Sherlock eats all of John’s food as well as his own and sleeps for the rest of the night in bed.

The next day Sherlock retreats to his mind palace and starts again. He finds an error in his data store and disappears to Russia for two weeks.

  
  
Lestrade finally asks John about Sherlock and Molly, a week after the Consulting Detective dashes off to Asian continent. Mycroft overhears the question and reminds the older man that even Sherlock Holmes is prone to human error.

John reminds him that Moriarty swore to burn the heart out of Sherlock on their first meeting.

 

Mycroft joins his brother in Russia the next day.

 

**_To be continued..._ **

 


	2. Part 2

**Summary for the Chapter:**

> It takes two years to find Molly and three weeks to rescue her.

_No rights to this.  It's all the BBC's, I just play with them._

** **Part 2** **

 

It takes two years to find Molly and three weeks to rescue her.

It’s a joint effort between Sherlock, Mycroft and Mary. John doesn’t know exactly what they did and has told himself that he doesn’t want to either. He’s a soldier, he knows war is a brutal and the casualties are many. He cannot imagine how in anyway it can be good to know what those three can do combined.

He does know that it take several weeks for anyone to be allowed to see her and even then it’s with restricted access. He finds out why on his first visit when Mary has to subdue Molly from shoving her IV in his throat. Molly is frighteningly different and it terrifies him when he cannot see the old Molly at all. John feels stripped to the bone when she assess him, her eyes calculating and mindful. It’s after Mycroft takes him aside and explains her current track record with unsupervised personnel, (apparently she’s very handy with a scalpel) that he realises that she reminds him of hunter, waiting to strike.

Molly is not the same woman she once was and John doesn’t realise until he sees the her in the cold light of day, how much he was expecting her to be. That night, in bed and in the dark, Mary holds him as he cries for the loss of his friend.

 

The Doctor screens Lestrade’s calls for the first 6 months of Molly’s return. Sherlock doesn’t take on a single case during this time. He spends everyday with her, trying to coax the truth of her imprisonment, one secret at a time. It's common knowledge that he has scars from her attempts to get at him. Later it emerges that it’s all a compromise; a scar for each secret. John doesn’t approve of the therapy, when he does become privy to the information, but patches his friend up anyway. Mary, however, does understand and often reminds her husband that none of Sherlock’s relationships are conventional.

When the ‘therapy’ hits a standstill Sherlock takes a level 4 case in frustration and it takes him far longer than it should to solve. In the end Anderson intervenes at Donovan’s insistence and helps Greg catch the criminal. It does not go unnoticed that Sherlock disappears before the case is solved and doesn’t visit Molly.

When sighting and rumours start to surface about the detective being spotted in Eastern Europe, Mycroft disappears too. John remains puzzled until Mary mentions in passing that Moriarty is supposedly hiding out there. He doesn’t follow but instead goes to see Molly.

  
  
His first visitation after Molly was discharged from the hospital was awkward to say the least. It also wasn’t very long. The subsequent visits are longer but it is mostly to bring Tobey to visit Molly, since he can’t stay at the clinic with her. Tobey is initially as suspicious of Molly, as she is of him. It’s only an apparent and mutual distrust of Sherlock that seems to bring them back together.

Molly looks healthier now, nowhere as wild as before, but there is still calculating look in her eyes. She eyes him in the beginning with curiosity and suspicion. He doesn’t really blame her, he hasn’t spent much time around her since her return (except as a first aider) and they were not the closest of people before her abduction.

She never mentions Sherlock’s absence during those months he’s gone and John is fairly relieved about that. Their time together is spent mostly in silence, occasionally it is filled with the rustle of his newspaper and her playing with Tobey. It’s not the most exciting way of spending time with someone, but John likes to think that his being there is a small comfort.

When Sherlock does return, he avoids Molly and takes on several of Lestrade’s cases. He solves them all quicker than ever before and takes on every private case that comes him, no matter how tedious they are. It doesn’t take a genius to work out that the trip was a wasted endeavour.

 

It’s raining when Molly finally asks why Sherlock is avoiding her.

Tobey had been left at home as he hates storms and the room is filled with a deafening silence. John resents his inability to fill it, the tension making him itch and suddenly he sees out why Sherlock is so desperate to try to fix her. He is overcome with how much he really does miss the old chatty Molly. The quiet is a stark contrast to the old days and without warning John finds himself speaking to her about everything. If you asked him today what he said, he would honestly reply that couldn’t remember, the whole scenario is similar to an out of body experience. He knows that speaks of her disappearance and through the years she was gone. The memories and events she has missed and cases that have passed. He speaks of his family and his marriage.

It’s turned dark long before he talks of Sherlock, of his friend’s sadness and unflinching relentlessness to find her. It’s easier to speak of it in the dark, like its a secret that he shouldn’t be sharing. The words come leaving Sherlock’s heart laying bare and Molly listens. She never moves. Never stops looking out the window. He can’t tell if she hears him and there is no sign of acknowledgements, but the Doctor has spent so many years with Sherlock that he knows appearances are deceiving.

John feels lighter when he leaves. The rooms tension has cleared, like the sky after a storm. He doesn’t know if what he has done will help but he just hopes that he’s cut away enough of the scar tissue from the wound so regrowth can now happen.

 

It’s Molly that goes to Sherlock first.  John walks in to 221b Baker Street to find her sitting in his chair and drinking tea. Tobey curled in her lap. John wonders if she has her protection detail in tow but a text from Mycroft informs that she no longer needs one. He knows that his brother is more than equipped to deal with the former Pathologist. Mary’s smile when she comes round later that day, toddler in tow, tells John to shut up and enjoy himself.

That is exactly what he does when Sherlock starts experimenting with his two-year old and teaching her new words. Molly spends the entire time watch from her perch, seemingly entranced with their interaction. The Consulting Detective has a uniquely brilliant way with children and his daughters laughs of delight at “ _silly Unkol Sher_ " are pure delight.

It doesn’t go unnoticed by any of them when Molly leaves that Sherlock’s eyes follow after her with rapt attention.

  
  
**_To be continued..._ **

 


	3. Part 3

**Summary for the Chapter:**

> It was an universal truth that there was only one woman the Holmes brothers would never cross.

_I don't own anything, I just borrow them._

**Part 3**

  
It was an universal truth that there was only one woman the Holmes brothers would never cross.

John had never pegged Mummy Holmes as the terrifying type. The way the two brother spoke about her often gave the impression of a weak and feeble woman who was prone to fits of melancholy. 30 seconds in the woman’s presence obliterated any thoughts of that and replaced it with the simple fact that ‘Mummy’ was not a woman to be underestimated in the slightest. Bona fide genius and more sneaky than a ninja in the dark, she made Sherlock and Mycroft look like amateurs. John adored her for it. It did not take long into their acquaintance for him to understand the keen protectiveness her son’s felt over her, he felt the same.

John would never admit (even under threat of torture and death) that he would have been jealous of their father had he been 20 years older. Even Mary had openly admitted that she could see where Sherlock got his _mysterious_ appeal from.

What was noticeable, in the short time the Doctor had got to know his best friend’s mother, was how much she did love her children. There was no denying the aloof and sometimes austere attitude to people that her sons had in no doubt inherited, but it wasn’t a cruel. John could imagine that raising two boys like Sherlock and Mycroft had undoubtedly left a mark. Just like his relationship with the curly-haired robot, it could sometimes be difficult to get back the emotion you put in to it.

So when Mummy Holmes met Molly Hooper, roughly a year after her return, no one could have predicted the immediate and inseparable bond that instantaneously sprung up between the two women. John to this day would never be able to tell you who was more shocked, him or her sons.

  
  
Molly had become a firm fixture to Baker Street following the breakthrough several months earlier. Things between the former Pathologist and the Consulting Detective had mended and grown at a blinding rate. She had begun helping with experiments and tagging along with Sherlock on the cases that John was unable to assist. It seemed a small consolation for the fact she would never be allowed back to her old job. John had never been brave enough to ask her how she felt about that, but he could probably guess the answer. Molly had been exceptional at her job and unsurprising in regards to how young she had been when she got it. It made sense though, given her lack of options for employment now, for her to join Sherlock on his escapades and the detective certainly didn’t seem to mind.

It was a relief to John, Sherlock gaining a new assistant, as the the Doctor’s position at the Practice had become more important over years and that his list of responsibilities had increased. He was also a father and a husband (damned good one too on both counts) and had a life outside of solving crime. Sherlock had understood this without too much difficulty and selflessly given John the space needed. Mary helped out too when she could but she also needed time with the family and she often found the lifestyle too close to her old life to stay in it too long. Sherlock would have his moments though and the Watson’s had accepted long ago that there would always be calls late into the night or experiments used on their child (that went with the territory), but it helped that John had an extra pair of hands to help with his friend.

It was a genuine surprise that Molly had brought a reasonable level of normalcy to the flat after she moved in, much to Mrs Hudson’s delight. The landlady had been wary of Molly and there had been a risk that Mrs Hudson would have refused her a tenancy. Mrs Hudson wasn’t the only one to have her doubts, but she was the loudest in voicing them. It was to be expected after everything that had happened during her stay at the clinic, not to mention the damage she inflicted at the hospital. It didn’t take long for everyone to warm to her living with Sherlock, though John could guess the fact that Mrs Hudson no longer had to clean up after Sherlock warmed her to Molly’s presence in the building. Molly Hooper also seemed to have the extraordinary ability to silence Sherlock with a single look, which came in remarkably handy when the clients were round.

It had been mostly been Mary behind getting Molly into Baker Street and in hindsight it had been logical. 10 months after her return and 2 months after her and Sherlock were back on speaking terms, the medical staff had announced their patient well enough for a discharge from the Clinic and the question of where she would go became a pressing issue. Mycroft voiced that it may be best to put her to be put into home, after all he was still wary of her state of being after such an experience. Mary had argued that Molly had spent long enough in captivity and John had debated how productive any of this was going to be for her. The discussion got heated and it was only when Molly had stormed upstairs and slammed the door had they all realised she had overheard. Sherlock had rolled his eyes and reminded them that he was supposed to be emotional idiot of the group and went after her, pilfering two teas and the chocolate biscuits on his way up. When Molly was eventually coaxed back down, Mary had then suggested Baker Street. John nearly choked on his tea at Lestrades’ face when Sherlock asked her how quickly she could move her stuff in.

The move had been quick and almost stress free. However John noted the installation of a lock on the bathroom door and had chuckled to himself, Sherlock had never got the hang of privacy.

  
  
It was nearly Christmas when Mr & Mrs Holmes popped into Baker Street to visit their wayward son, Mycroft in tow, and met Molly Hooper for the first time.

Mycroft had warned Sherlock of their parents threat to visit. Apparently they had been understanding, but not happy, that their sons had both left abruptly the Christmas before.  With so much excitement of locating Molly and getting her home, the brothers has both successfully avoided what they dubbed “that pagan holiday of misery” with the family.  When the Mummy Holmes reminded them of the threat, it had been dubbed “unimportant” by Sherlock and then promptly deleted.  He (begrudgingly) admitted to John much, much later that he had made a terrible error in doing this.  

So when the Holmes finally decided to make good on their threat, they could not have picked a worse time.  The two friends had been dealing with a particularly gruesome case, concerning a serial killer with a taste for mutilating the victims before death.  It had taken the best part of a month and none of the group had slept or eaten properly.  Tensions were high, Sherlock had taken up smoking again and Lestrade had banned everyone from calling him when it finally broke.  They had caught the duo responsible and everyone had crashed at 221b for dinner.  
  
By the time Sherlock’s parents had arrived Molly had already manhandled the majority of the group home. Lestrade had been bundled into a taxi, Mrs Hudson was downstairs with one of her _herbal soothers_. John had been completely envious of her ability to function but that had disappeared upon the realisation that Molly was going to be the one to deal with the exhausted Consulting Detective. Waiting patiently for their taxi, The Watsons’ watched with bemusement at Sherlock’s quiet submission. If John hadn’t been so tired he would have recorded his friend’s behaviour, particularly when he hung on the petite brunette and attempted to snuggle in her neck like a kitten. John would not be reminding his wife that he owed her £20. He should have known Mary would be right about the lanky bastard being a _snuggler._.

John would never, _ever_ forget the look on the Holmes’ faces when they entered the flat to find Molly ordering a half-comatose, but totally compliant, Sherlock into bed.

  
  
The next morning, having cited exhaustion the previous night and bolted out of the door, John and family in tow, entered 221b to a very excited Mummy Holmes loudly expressing a wish for one of her sons to marry Molly Hooper, before she did.

Later, when questioning Mr Holmes on the outburst, John learnt that Sherlock had slept for a full 8 hours, ate breakfast without complaining, held a decent conversation with his parents about their holiday in Australia and been completely civil to Mycroft for the entirety of the morning. He also learnt that Mr Holmes was as big of a fan of Molly as his wife was, but for totally different reasons, Molly had promised him a copy of all her research she had been working on over the years. Guess where the eccentric detective gets his interest in the unusual from…

Before the day was through Molly had been asked (demanded) to go to dinner with the Holmes with both of the Holmes children promising they would attend. John laughed out loud, receiving a poisonous look from them, when Molly agreed she would make sure they would.

When they arrived at the restaurant, smartly dressed and on time, Mummy Holmes asked Molly what she was doing for Christmas.

 

**End of Part 3**

 


	4. Part 4

**Summary for the Chapter:**

> No-one seems to want to discuss the elephant in the room.

_ **Warning:** _ __ __This chapter is dark and has some possible upsetting themes for some readers so please, if you feel uncomfortable, don't feel that you have to continue._ _

**  
** ** **Part 4** **

 

No one seems to want to discuss the elephant in the room.

Molly doesn't blame them, after all it's not like she wants to talk about it either and she is pretty happy with the arrangement.  She point blank refuses to discuss her time in captivity.

It would destroy whatever is left of her if they discover that she's can no longer be considered human.

  
  
When they rescued her, she was sure it was a hallucination.  It wouldn't have been the first time, her captors had seemed to find joy in giving her false hope.  It took far longer into her abduction than it should have for her to accept that hope was going to get her killed.  She had sat there and waited for the illusion to shatter, attacking anyone who came near her.

It takes a long time for her to acknowledge the reality of her freedom.

The Doctors are optimistic of her recovery, to a degree at least.  There is often the discussion that she will regain some parts of her former life.  Her former career however will forever be shut to her but she had already known that.  She would never be able to handle dealing with the dead after being with of them for so long.  She knows she should be angry and enraged at what has been taken away from her, after all she was one of the bloody best at her job, but the emotions seem to clip through her fingers like sand.

The emptiness is all consuming and she wonders if she'll ever get back, even some, of the highly emotional person she was before.  She had been forced to kill that Molly very quickly into her capture.  Survival was her main priority.

  
  
She tries not to remember the first year.  Getting used to the darkness had been the hardest adjustment.  Eventually it became her best friend, hiding her from the others and embracing her like lover.  It was her comfort for those years and now she much prefers the darkness to the light.  The  _prison_ they had thrown her in had been some form of cave network with no natural light and a labyrinth of corridors.

Her kind and loving nature had been a hindrance, something she found out two weeks in her imprisonment when she helped the wrong person.  She can still feel them over her when closes her eyes.

Her next lesson had been to map the complex and remember the safe spots.  She had learnt that one the quickest, the few times her memory failed her, had catastrophic results.  Though it has to be said, her education as a doctor has given her the advantage at incapacitating her attackers and leaving a lasting impression.  By the time of her rescue, very few inmates bothered her.

She has scars though, from those encounters, the most obvious is the jagged puckered skin reaching from the back of her neck to the corner of her shoulder blade.  She feels her face darken at the memory of the slight Russian's face as he pulled the steel along her body but smiles at the bastards expression when she severed his  _man parts_  and fed them to his dog.  Some days she feels like the scar was worth it.  She still has no idea what his name was though.  The other scars aren't as big, but bright white lines coat her body like a dot-to-dot.  She remembers with crystal clarity exactly where every single one came from.  She had to, they were the lessons she needed to learn.

  
  
She knows they are trying, always trying, to help bring parts of her back.

John sits with her every Thursday, like clockwork (Mary has to work and their daughter is at nursery) and brings Tobey for her to play with.  Its quiet, save for his rustling newspaper and her cats playful attempts to steal the bottom of it.  Its not the most fun someone can have on a Thursday but at least she isn't being assessed by the psychotic therapist the Clinic have set her up with.  She's fairly certain the  _good doctor_  should be in here with her.

She and John had never really been close, even before her little  _holiday_ abroad.  He was always kind though and at one point she was sure if she hadn't been so hung up on Sherlock she would have jumped him for sure.  It's laughable now, John is nowhere near her type.  She's always had a thing for the psychos.

Especially now she's one too.

Mary visits her and somehow manages to sneak her out to the local pub down the road.  They have an unusual friendship.  The blond is the only one who doesn't shy away from who Molly is now, if anything she seems to encourage more of the darker bits of her new personality.  She shows Molly how to hone her skills and use them in a  _non-lethal_ capacity.  The other woman confessed that she wishes she had taught Molly before.  The former Pathologist merely finished her drink in response and patted her hand in as a form of comfort.  Mary had then perked up and asked her how she felt about guns.  Molly had excitedly grabbed her hand and pulled her out of the pub.

After all she wasn't going to turn down shooting tips from a trained assassin.

She does see the others and occasionally it's in an official capacity.  She's fairly certain Mycroft and Lestrade haven't quite forgiven her for her attempts to gut them with a scalpel, during those first days in the hospital.  Lestrade does visit her a few times when she's moved to the Clinic.  It's always under the guise of updating his records, but they never talk about case, only the merits of a decent football game.

Mrs Hudson doesn't visit though and when Molly moved into 221b, the landlady confessed that she didn't like the smell of hospitals and the Clinic reminded her of her future in a care home.  Molly could begrudge her that and promptly informed the woman that Baker Street was her home and always would be.  It wasn't a coincidence that the older woman was happier to have her around after that.

She never tells anyone about her and Mycroft's monthly chess game, not even his brother.  It's a commitment that continues after she moves into Baker Street and she enjoys keeping it from the Detective.  Her and Mycroft have a bet going over how long it will take him to work it out.  She suspects that he might be cheating, when he starts threatening to swear her to secrecy.

It gives her unparalleled joy to know she's better at chess than he is.

  
  
  
They never ask her about what happened, but of course, Sherlock Holmes dances to his own tune.

The bastard has to know everything.  He has no qualms in digging through her scars so hard that he hits bone.  She's a puzzle that he needs to solve and everytime she tries something from him, he tries to get to it a different way.  He strips her bare and leaves the nerves raw to the world.  The process drags up all the emotions she had buried and she can't control her instinctive nature to lash out.  Everytime she hits him she wants to take it back, but he revels in it and pushes her again.  It's relentless, the cycle they become trapped in and she knows deep down that this is doing more damaging than good.

She hadn't meant to hit him the first time.

In truth it had been an accident.  When she'd  _finally_  seen Sherlock for the first time, she had felt nothing.  Panicking she'd lashed out and caught him with her flailing limbs.  When it had registered what she had done, some small part of her had briefly hoped it would awaken something that had long been dead.  When she'd felt nothing, she had done it again and again until arms held her down and something scratched at her neck.  The last thing she had heard was Sherlock insulting the hospital staff before the sedative took her down.  She had willing embraced the darkness, after all she'd lived in it for so long, it was an old friend.  She remembers an acute aversion to the brightness of the ward.   It was harsh and alien, and all she'd wanted to do was claw her eyes out and tear at the restraints holding her down.

She'd fucking hated that hospital.

She relents the  _light_  stuff, the events that have happened that don't bother her to tell him.  Its not what he's asking for and he gets frustrated easily at the lack of progress.  She can tell he's taken up smoking again, the itch in his fingers to spark up and draw the smoke into his lungs.  She wants to hate herself for what she is clearly doing to him, to give up and tell her tale of woe.  After all, he knows how bad it would have been, he sees it everyday and knows the brutality of humanity.  She won't give in though.

She still loves him too much to do that.

It doesn't take her long to work out what Sherlock is doing.  How he's using their  _therapy session_  to punish him for failing her in the first place.  It does take 6 months for an old version of Molly to rise through the endless emptiness and bring it all to an end.  She doesn't talk to him again and she doesn't lash out.  She isn't surprised when he disappears.

She's more concerned as to how the old Molly can still be alive.

 

She misses him.

More than she thought she would and the months of his avoidance drag.  John is itching to fix it, his knee jiggles when he stops reading the newspaper but she ignores and continues to play with Tobey.

She lasts 3 months until its Autumn and the British weather comes with it forcing John to visit without her beloved pet.

The weather is bad, even for England and the trees thrash in the wind.  She was surprised John bothered to venture out to see her, she wouldn't have.  The rain lashes against the window filing the room with some noise to break the awkward tension.  John gave up reading his newspaper when the lightening started and joined her in staring out the window.

She can see him watching her in the windows reflection, he can't see her doing it and it allows her the opportunity to study him.  Too long has she spent watching her back to stop doing it now.  He's deep in thought, analysing her like a suspect and he suddenly looks at her the same way Sherlock has since her return, like there should be a way to fix her.  The temptation to punch him in the throat is hard to subdue.

They should know by now that she's beyond repair.

When John suddenly starts talking about their lives during her disappearance, the urge disappears and all she can do is listen.  She doesn't move from her position, but she watches every expression that crosses his face.  The heartbreak when he realised she was missing, the regret when they failed to find her.  She takes in the anger and hopelessness as they struggled to find her over the years.  Molly wants to feel betrayed when he talks about his family and all the stories that have happened without her, but she doesn't.  It nice to know there was good happening while she was away.

In a perverted way it feels like her suffering was worth it.

 

In the darkness he speaks of Sherlock, and Molly has to fight every muscle in her body not to turn round and absorb the words like water.  It feels safer, she would admit, to hear of him in the dark and strangely fitting.  John talks as if he's revealing a secret he wasn't meant to share.  His words stroke something within her, an emotion she hasn't felt in a long time and for once she isn't so frightened.

John's expression throughout is one that she doesn't recognise and it bothers her more than it should do.

When he's finished and gone, the room feels like its been cleansed.   _She feels different_  and his words echo through her mind for the rest of the night.  She doesn't sleep, she can't, so she sneaks out on to the roof and into the storm.  By the time the storm has calmed and the morning comes Molly is already at Baker Street.

When John and his entourage enter the flat later in the day, his smile doesn't escape her notice.

 

**End of Part 4**

 

__So this is probably the hardest chapter I have ever written and it still doesn't sit right with me but I had to get it out for all you amazing people who have been reading it. <3_ _

 


	5. Part 5

**Summary for the Chapter:**

> There were times when Molly wished they would stop acting like she was made of glass

_As always I have no rights to these amazing characters_

_ **Part 5** _

 

There were times when Molly wished they would stop acting like she was made of glass. The condescending belief that she was unable to look after herself really does try her new-found patience of _not killing people_.

She almost preferred it when they were afraid of her.

She vaguely notes the whiting of her knuckles as she refrains from burying the butter knife, she is currently holding, into the side of Mycroft’s skull. From the concerned glances her dark-haired companion keeps giving her, she quickly realises that she isn’t as good at hiding it as she used to be.

_Damn._

When she walks in to the living room with the tea tray and her arms starts to tremble from the strain of holding back, she snaps and slams the tea tray on the table before storming off to John’s old bedroom. She already knows that Sherlock will follow her shortly. He always does.

She just hopes he brings the biscuits with him.

  
  
John's old room has become a haven, during the time she has started frequenting Sherlock’s flat for their ‘get-togethers’. It was useful sometimes, to hide away in the dark and calm down when things get intense. She is still no better at handling large crowds or certain _types_ of clients. When he gets submerged into his mind palace, she finds it a comfortable place to read as she's never sure if pottering around the flat disturbs him, so she leaves him be. He usually comes to her when he's finished and sometimes she'll return from her own imaginary world to find Sherlock asleep next to her.

John's old room is a neutral ground and sometimes more breakthroughs happen here then anywhere else.

She has no idea what to call their meetings now. After all they have progressed far beyond simply talking about her past and have moved forward to something _different._ Sometimes she helps him with cases, other times she goes through his _experiments_ and removes the ones that have long expired past anything useful. He's starting coming to her with queries about his lab work and she has never been so thankful for her natural aptitude for science. He does glare at her when she removes the old experiments, but she hates how the smells reminds her of _there_ and she can handle his hissy-fits better than the flashbacks.

  
  
She hadn’t told anyone about them. The flashbacks. Not even her therapist that she is still required to see once a week, mind you she doesn't really tell the noisy bastard anything. She keeps them all locked up far below herself, in the darkness, where they can’t get out.

Along with _her._

_The clock is ticking._ It’s been the thought that has been haunting her the most lately. Sherlock has even commented on her lack on interaction and she hadn’t been lying when she told him that she has bad days coping. She just can't tell him that the clock is ticking for old Molly’s return and it scares the living shit out of her. It's something that she just cannot cope with in the slightest.

She wants to tell someone, anyone, that lately she had been getting in an increasing number of incidents with the old Molly. That she can feel her floating beneath the surface of her cell. The walls flex at the pressure and the self-imposed imprisonment doesn’t always feel as secure as it used to. There are cracks, small tears which allows the whisper of hope to escape and she wants to cry at the injustice of it all. She helped them survive, to escape the hell they went through and now that they are home she is going to be _deleted_. It is, after all, common knowledge among the group that it had been a necessary sacrifice by Molly to lock herself away so that she may survive. During her time in recovery most now believed her to be dead, but the truth was that she had been buried so deep that the new Molly had thought she had been lost forever to the nothingness.

It had been an error to believe that her former self was too weak to fight her way back.

  
  
Sherlock had brought the biscuits.

She had smiled when he plonked himself down unceremoniously next to her and hoovered half the packets in the time it took her to eat one. She, like many people, had previously believed him to eat sparing. Especially considering how skinny the bastard was. That opinion quickly changed at the sheer about of food he could put away in a short time. She had learnt to hoard her portion of any sweet-related foods as she wouldn't get a look in if he found them. When he began eyeing up her biscuits she jokingly growled at him, he still managed to steal one.

As the noise downstairs escalated, her companion grabbed the nearest book from the floor and placed it in her hands with an imploring look. She doesn't skip a beat whilst narrating the third chapter of the book, when a head landed on her lap and her fingers found his hair. She does let the giggles slip when Sherlock gets excited at the mention of dragons and pats his head in sympathy at his annoyance when Harry beats it. She should have pegged him as a dragon fan. She briefly wondered how he would take The Hobbit if she read that to him.

He would make an incredible Smaug.

When the noise below quietens she closes the book and they re-emerge into the deeply apologetic group below.

  
  
There was both good and bad sides to moving into Baker Street.

For the most part Sherlock is, surprisingly, a creature of habit and she can predict some sort of routine for maintaining the cleanliness of the flat. When it came to feeding, she knew that if she put food in his proximity (obviously around cases) then he would eat it. She quickly worked out how long most of his experiments could hang around before becoming toxic and which ones she could 'touch' before Sherlock complained. Above all, it didn't take long for her to figured that underneath all the clutter, the place was actually very clean and if Molly had missed cleaning something Mrs Hudson would catch it. Of course, he never cleaned the bathroom after himself and the towels would always be strewn across the floor, but men will be men.

The downside to sharing with someone like Sherlock, was his typical approach to life, which was at the expense of other people's privacy. She sometimes would find him in her room going through her stuff in search of _something_ for one of his cases. If she hadn't made enough food on one of his post-case binges, the greedy bastard would eat her portions as well and now she always made extra. She did invested in another fridge when she realised that Sherlock's experiments were expanding beyond their designated sections and could very easily cause someone to get ill very quickly. Even now Molly cannot work out how John lived with one fridge for so long. She had also invested in a lock for the bathroom when it became a regular occurrence for him to walk in when she was in the bath.

The first time had been awkward, the fourth annoying and the sixth time Sherlock had found himself sprayed down with the shower hose.

  
  
Molly knew that Sherlock had caught glimpses of the old Molly. Living together meant that this was always going to be an inevitability. The look of hope that she can see in his eyes whenever she slips up is getting more and more frequent.

But doesn't mean that it gives her any comfort.

There are days when the Molly below is more active inside her prison, than others. She claws at the walls while Sherlock dug relentlessly from above. It wouldn’t take long for the both of them to find a way to release her. The truth is Molly isn’t afraid to let her former self out, actually she is excited to feel anything again instead of the nothingness that had consumed her for so long. Her fear was letting it all out.

The truth included. The memories and the darkness that was trapped down there as well. There was something lurking beneath it all that frightened both of the Molly’s collectively which is why, on the bad days, her former self doesn’t fight the prison she has been placed in. It had been a sacrifice by them to lock herself away so deep that the new Molly had thought she was lost forever to the nothingness.

It had been an error to believe that Molly was too weak to fight her way back.

  
  
Dr Molly Hooper was the strongest and most determined woman to walk the earth and she was determined to come back to the world and the people she loved.

  
  
**End of Part 5.**

 


	6. Part 6

**Summary for the Chapter:**

> Taken from the amazing review by Rocking the Redhead
> 
> It was so hard to accept that they had broken her. Finding the old Molly that was still inside was going to be difficult.

_ **Part 6** _

_   
_ _ It was so hard to accept that they had broken her.  _

Mary had known that when she saw Molly that first time. At first she hadn’t believed the images that Mycroft had shown her were of the mousey brunette she had known all those years before. She felt the sudden emptiness fill and she knew that the Holmes brothers weren’t going to rescue the much sought captive without her. The Assassin that she had thought she had buried, clawed to get out and the immediate urge to grab a gun, had been almost too hard to ignore.  It wasn’t until she had fake ID’s in her hand that she realised that she had succumbed to the Assassin’s desire to be free.  

She had kissed John and bid Mr & Mrs Holmes adieu. She wouldn’t look at her daughter, not with the bitch inside sneering at how human she had become.

She really hated her, but right then she needed her more.

  
  


Even now, after every step of Molly’s struggle to recover some sense of normalcy (well… for her), whenever Mary sees a falter,  she is never ready for the surge of rage and protectiveness.  She is not a fool and knows that Molly now has the ability to protect herself, no matter the cost, but she’s family.  

Mary loves her family and no-one threatens it.  

Sherlock understands it.  After all she shot him to protect John.  She thinks he feels the same way.  If she ever became a threat to John, she knows Sherlock would put a bullet in her too.  

Mutual respect at its absolute best. 

  
  


When she sees the others struggle to cope with the “new” Molly, she wants to hit them all over the head with a frying pan.  Sometimes she swears they think one day she’ll wake up and suddenly old Molly will be back.  ”Old” Molly… with her cute ponytails and shy disposition.  

They must be joking. 

"New" Molly is a feral killing machine wrapped in a fragile shell of confusion and frustration.

They’re lucky she hasn’t stabbed them in their sleep for acting like they somehow have a choice in what she does.  Surely they know men never have a choice in the actions of women.  Particularly the crazy or damaged ones.  In Molly’s case, both.  

  
  


The argument for future accommodation was never going to be won by anyone other than Molly.  Even Sherlock had seen that, some what surprisingly.  It had been enjoyable to see the other’s face to Sherlock’s stand of solidarity to Molly rather than trying to manipulate the room to his own opinion.  

Who would have thought that Sherlock Holmes could be human… without it being for something he wanted.  

  
  


It does occur to Mary much later that maybe Sherlock had known his reaction would get the result it did.  Which means he had wanted it to end up like that.  That is something that even she is unprepared to spend time thinking over.  

In the end, she surmises that the reality is that the Detective is just lonely and Molly does have a PHD.  They can play to their hearts are content… That or their conquest for world domination is complete. 

Either way, John will be allowed to come home on a regular basis and that suits her just fine.  Mycroft can surely handle whatever they throw at him.

Hopefully…

  
  


**End of Part 6**

  
  


_Ahhh it’s so short.  I am a bad author. Guys, I am so sorry it’s taken me so long to update… April. Opps.  Studying to be a lawyer is way too consuming for fanfiction! Thanks again for sticking by and hopefully you won’t have to wait so long for the next one._

_TTFN! xxx_

 

 


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